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Reid N, Reyne MI, O'Neill W, Greer B, He Q, Burdekin O, McGrath JW, Elliott CT. Unprecedented Harmful algal bloom in the UK and Ireland's largest lake associated with gastrointestinal bacteria, microcystins and anabaenopeptins presenting an environmental and public health risk. ENVIRONMENT INTERNATIONAL 2024; 190:108934. [PMID: 39106632 DOI: 10.1016/j.envint.2024.108934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 08/09/2024]
Abstract
Harmful Algal Blooms (HABs) are outbreaks of aquatic toxic microalgae emerging as a global problem driven by nutrient enrichment, global climate change and invasive species. We uniquely describe a HAB of unprecedented duration, extent and magnitude during 2023 in Lough Neagh; the UK and Ireland's largest freshwater lake, using an unparalleled combination of satellite imagery, nutrient analysis, 16S rRNA gene sequencing and cyanotoxin profiling. The causative agent Microcystis aeruginosa accounted for over a third of DNA in water samples though common bacterioplankton species also bloomed. Water phosphate levels were hypertrophic and drove local algal biomass. The HAB pervaded the entire ecosystem with algal mats accumulating around jetties, marinas and lock gates. Over 80 % of bacterial DNA isolated from algal mat samples consisted of species associated with wildfowl or livestock faeces and human-effluent wastewater including 13 potential pathogens that can cause serious human illness including: E. coli, Salmonella, Enterobacter and Clostridium among others. Ten microcystins, nodularin and two anabaenopeptin toxins were confirmed as present (with a further microcystin and four anabaenopeptins suspected), with MC-RR and -LR in high concentrations at some locations (1,137-18,493 μg/L) with MC-LR exceeding World Health Organisation (WHO) recreational exposure guidelines in all algal mats sampled. This is the first detection of anabaenopeptins in any waterbody on the island of Ireland. Notwithstanding the ecological impacts, this HAB represented an environmental and public health risk, curtailing recreational activities in-and-around the lake and damaging local businesses. Reducing agricultural runoff and discharge from human-effluent wastewater treatment to manage nutrient loading, and the public health risk, should be the top priority of stakeholders, especially government. Key recommendations include Nature-based Solutions that avoid conflict with the productivity and profitability of the farming sector enhancing sustainability. We hope this stimulates real-world action to resolve the problems besetting this internationally important ecosystem.
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Affiliation(s)
- Neil Reid
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, Northern Ireland, UK.
| | - Marina I Reyne
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, Northern Ireland, UK
| | - William O'Neill
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, Northern Ireland, UK
| | - Brett Greer
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, Northern Ireland, UK; International Joint Research Center on Food Security (IJC-FOODSEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
| | - Qiqi He
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, Northern Ireland, UK; International Joint Research Center on Food Security (IJC-FOODSEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
| | - Oliver Burdekin
- Department for Continuing Education, University of Oxford, Rewley House, 1 Wellington Square, Oxford OX1 2JA, UK
| | - John W McGrath
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, Northern Ireland, UK
| | - Chris T Elliott
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, Northern Ireland, UK; International Joint Research Center on Food Security (IJC-FOODSEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
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Yu Y, van der Donk WA. PEARL-Catalyzed Peptide Bond Formation after Chain Reversal by Ureido-Forming Condensation Domains. ACS CENTRAL SCIENCE 2024; 10:1242-1250. [PMID: 38947204 PMCID: PMC11212132 DOI: 10.1021/acscentsci.4c00044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 07/02/2024]
Abstract
A subset of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are encoded in their biosynthetic gene clusters (BGCs) with enzymes annotated as lantibiotic dehydratases. The functions of these putative lantibiotic dehydratases remain unknown. Here, we characterize an NRPS-PKS BGC with a putative lantibiotic dehydratase from the bacterium Stackebrandtia nassauensis (sna). Heterologous expression revealed several metabolites produced by the BGC, and the omission of selected biosynthetic enzymes revealed the biosynthetic pathway toward these compounds. The final product is a bisarginyl ureidopeptide with an enone electrophile. The putative lantibiotic dehydratase catalyzes peptide bond formation to a Thr that extends the peptide scaffold opposite to the NRPS and PKS biosynthetic direction. The condensation domain of the NRPS SnaA catalyzes the formation of a ureido group, and bioinformatics analysis revealed a distinct active site signature EHHXXHDG of ureido-generating condensation (Curea) domains. This work demonstrates that the annotated lantibiotic dehydratase serves as a separate amide bond-forming machinery in addition to the NRPS, and that the lantibiotic dehydratase enzyme family possesses diverse catalytic activities in the biosynthesis of both ribosomal and nonribosomal natural products.
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Affiliation(s)
- Yue Yu
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Owens SL, Ahmed SR, Lang Harman RM, Stewart LE, Mori S. Natural Products That Contain Higher Homologated Amino Acids. Chembiochem 2024; 25:e202300822. [PMID: 38487927 PMCID: PMC11386549 DOI: 10.1002/cbic.202300822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/13/2024] [Indexed: 04/11/2024]
Abstract
This review focuses on discussing natural products (NPs) that contain higher homologated amino acids (homoAAs) in the structure as well as the proposed and characterized biosynthesis of these non-proteinogenic amino acids. Homologation of amino acids includes the insertion of a methylene group into its side chain. It is not a very common modification found in NP biosynthesis as approximately 450 homoAA-containing NPs have been isolated from four bacterial phyla (Cyanobacteria, Actinomycetota, Myxococcota, and Pseudomonadota), two fungal phyla (Ascomycota and Basidiomycota), and one animal phylum (Porifera), except for a few examples. Amino acids that are found to be homologated and incorporated in the NP structures include the following ten amino acids: alanine, arginine, cysteine, isoleucine, glutamic acid, leucine, phenylalanine, proline, serine, and tyrosine, where isoleucine, leucine, phenylalanine, and tyrosine share the comparable enzymatic pathway. Other amino acids have their individual homologation pathway (arginine, proline, and glutamic acid for bacteria), likely utilize the primary metabolic pathway (alanine and glutamic acid for fungi), or have not been reported (cysteine and serine). Despite its possible high potential in the drug discovery field, the biosynthesis of homologated amino acids has a large room to explore for future combinatorial biosynthesis and metabolic engineering purpose.
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Affiliation(s)
- Skyler L Owens
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Shopno R Ahmed
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Rebecca M Lang Harman
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Laura E Stewart
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Shogo Mori
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
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Yu Y, van der Donk WA. PEARL-catalyzed peptide bond formation after chain reversal during the biosynthesis of non-ribosomal peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.23.573212. [PMID: 38187666 PMCID: PMC10769383 DOI: 10.1101/2023.12.23.573212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
A subset of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are encoded in their biosynthetic gene clusters (BGCs) with enzymes annotated as lantibiotic dehydratases. The functions of these putative lantibiotic dehydratases remain unknown. Here, we characterize an NRPS-PKS BGC with a putative lantibiotic dehydratase from the bacterium Stackebrandtia nassauensis (sna). Heterologous expression revealed several metabolites produced by the BGC, and the omission of selected biosynthetic enzymes revealed the biosynthetic sequence towards these compounds. The putative lantibiotic dehydratase catalyzes peptide bond formation that extends the peptide scaffold opposite to the NRPS and PKS biosynthetic direction. The condensation domain of the NRPS catalyzes the formation of a ureido group, and bioinformatics analysis revealed distinct active site residues of ureido-generating condensation (UreaC) domains. This work demonstrates that the annotated lantibiotic dehydratase serves as a separate amide bond-forming machinery in addition to the NRPS, and that the lantibiotic dehydratase enzyme family possesses diverse catalytic activities in the biosynthesis of both ribosomal and non-ribosomal natural products.
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Affiliation(s)
- Yue Yu
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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Khánh CM, Van Quyen D, Van TTH, Moore RJ. Heterologously expressed SacP23, a novel bacteriocin from Paenibacillus polymyxa #23, is active against methicillin resistant Staphylococcus aureus. ROYAL SOCIETY OPEN SCIENCE 2023; 10:231119. [PMID: 38126065 PMCID: PMC10731318 DOI: 10.1098/rsos.231119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Antimicrobial peptides have the potential to be used in a range of applications, including as an alternative to conventional antibiotics for the treatment of bacterial infections of humans and animals. Therefore, there is interest in identifying novel bacteriocins which have desirable physico-chemical properties or antimicrobial activities. Paenibacillus polymyxa #23, isolated from a marine sponge, has wide spectrum antimicrobial activity against Gram-negative and Gram-positive bacteria. To explore the basis of this antimicrobial activity, the complete genome sequence of the strain was examined. Multiple genes predicted to encode antimicrobial peptides were identified. One gene was predicted to encode a novel sactipeptide bacteriocin, named SacP23. To confirm that SacP23 does have antimicrobial activity and to explore the antimicrobial spectrum of the peptide it was heterologously expressed in Bacillus subtilis. A cluster of eight genes, encoding a full complement of accessory genes as well as the structural gene expressed from the native promoter, was cloned into B. subtilis BS54A. The recombinant strain displayed antimicrobial activity against several Gram-positive bacteria, including multi-drug resistant Staphylococcus aureus. Heterologous expression of a whole gene cluster offers a powerful way to interrogate and resolve the various antimicrobial activities expressed by native strains that encode multiple compounds of interest.
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Affiliation(s)
- Châu Minh Khánh
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong, Loc Tho, Nha Trang, Khanh Hoa, Vietnam
| | - Dong Van Quyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Vietnam
| | - Thi Thu Hao Van
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia
| | - Robert J. Moore
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia
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Bérubé C, Guay LD, Fraser T, Lapointe V, Cardinal S, Biron É. Convenient route to Fmoc-homotyrosine via metallaphotoredox catalysis and its use in the total synthesis of anabaenopeptin cyclic peptides. Org Biomol Chem 2023; 21:9011-9020. [PMID: 37921761 DOI: 10.1039/d3ob01608k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Herein, we report the first solid-phase total synthesis of the natural cyclic peptide anabaenopeptin F and the use of metallaphotoredox catalysis to overcome the key challenges associated with the preparation of the non-proteinogenic amino acid homotyrosine contained in these peptides. Starting from L-homoserine, enantiopure Fmoc-protected homotyrosine was prepared in a straightforward manner by metallaphotoredox catalysis with N-Fmoc-(S)-2-amino-4-bromobutanoic acid and 4-tert-butoxybromobenzene partners. The prepared protected amino acid was used in solid-phase peptide synthesis to achieve the total synthesis of anabaenopeptin F and establish the stereochemistry of the isoleucine residue. Protease inhibition studies with the synthesized anabaenopeptin F showed inhibitory activities against carboxypeptidase B in the low nanomolar range. The high convergency of the synthetic methodologies paves the way for the rapid access to N-Fmoc-protected non-proteinogenic and unnatural amino acids and the total synthesis of complex bioactive peptides containing these amino acids.
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Affiliation(s)
- Christopher Bérubé
- Faculté de Pharmacie, Université Laval, Québec, Québec, Canada, G1 V 0A6.
- Laboratory of Medicinal Chemistry, Centre de Recherche du CHU de Québec-Université Laval, 2705 Boulevard Laurier, Québec, Québec, Canada, G1 V 0A6
| | - Louis-David Guay
- Faculté de Pharmacie, Université Laval, Québec, Québec, Canada, G1 V 0A6.
- Laboratory of Medicinal Chemistry, Centre de Recherche du CHU de Québec-Université Laval, 2705 Boulevard Laurier, Québec, Québec, Canada, G1 V 0A6
| | - Tommy Fraser
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 allée des Ursulines, Rimouski, Québec, Canada, G5L 3A1
| | - Victor Lapointe
- Faculté de Pharmacie, Université Laval, Québec, Québec, Canada, G1 V 0A6.
- Laboratory of Medicinal Chemistry, Centre de Recherche du CHU de Québec-Université Laval, 2705 Boulevard Laurier, Québec, Québec, Canada, G1 V 0A6
| | - Sébastien Cardinal
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 allée des Ursulines, Rimouski, Québec, Canada, G5L 3A1
| | - Éric Biron
- Faculté de Pharmacie, Université Laval, Québec, Québec, Canada, G1 V 0A6.
- Laboratory of Medicinal Chemistry, Centre de Recherche du CHU de Québec-Université Laval, 2705 Boulevard Laurier, Québec, Québec, Canada, G1 V 0A6
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Wang H, Wang N, Tan Y, Mi Q, Mao Y, Zhao C, Tian X, Liu W, Huang L. Paenibacillus polymyxa YLC1: a promising antagonistic strain for biocontrol of Pseudomonas syringae pv. actinidiae, causing kiwifruit bacterial canker. PEST MANAGEMENT SCIENCE 2023; 79:4357-4366. [PMID: 37417001 DOI: 10.1002/ps.7633] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND Kiwifruit bacterial canker (KBC) caused by Pseudomonas syringae pv. actinidiae (Psa) is the main limiting factor in the kiwifruit industry. This study aimed to identify bacterial strains with antagonistic activity against Psa, analyze antagonistically active substances and provide a new basis for the biological control of KBC. RESULTS A total of 142 microorganisms were isolated from the rhizosphere soil of asymptomatic kiwifruit. Among them, an antagonistic bacterial strain was identified as Paenibacillus polymyxa YLC1 by 16S rRNA sequencing. KBC control by strain YLC1 (85.4%) was comparable to copper hydroxide treatment (81.8%) under laboratory conditions and field testing. Active substances of strain YLC1 were identified by genetic sequence analysis using antiSMASH. Six biosynthetic active compound gene clusters were identified as encoding ester peptide synthesis, such as polymyxins. An active fraction was purified and identified as polymyxin B1 using chromatography, hydrogen nuclear magnetic resonance (NMR), and liquid chromatography-mass spectrometry. In addition, polymyxin B1 also was found significantly to suppress the expression of T3SS-related genes, but did not affect the growth of Psa at low concentrations. CONCLUSION In this study, a biocontrol strain P. polymyxa YLC1 obtained from kiwifruit rhizosphere soil exhibited excellent control effects on KBC in vitro and in field tests. Its active compound was identified as polymyxin B1, which inhibits a variety of pathogenic bacteria. We conclude that P. polymyxa YLC1 is a biocontrol strain with excellent prospects for development and application. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Hua Wang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
| | - Nana Wang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Life Science, Northwest A&F University, Yangling, People's Republic of China
| | - Yunxiao Tan
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
| | - Qianqian Mi
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
| | - Yiru Mao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
| | - Chao Zhao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
| | - Xiangrong Tian
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Forestry, Northwest A&F University, Yangling, People's Republic of China
| | - Wei Liu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
| | - Lili Huang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, People's Republic of China
- College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
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Mandhata CP, Bishoyi AK, Sahoo CR, Maharana S, Padhy RN. Insight to biotechnological utility of phycochemicals from cyanobacterium Anabaena sp.: An overview. Fitoterapia 2023; 169:105594. [PMID: 37343687 DOI: 10.1016/j.fitote.2023.105594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/12/2023] [Accepted: 06/17/2023] [Indexed: 06/23/2023]
Abstract
Cyanobacteria (blue-green algae) are well-known for the ability to excrete extra-cellular products, as a variety of cyanochemicals (phycocompounds) of curio with several extensive therapeutic applications. Among these phycocompound, the cyanotoxins from certain water-bloom forming taxa are toxic to biota, including crocodiles. Failure of current non-renewable source compounds in producing sustainable and non-toxic therapeutics led the urgency of discovering products from natural sources. Particularly, compounds of the filamentous N2-fixing Anabaena sp. have effective antibacterial, antifungal, antioxidant, and anticancer properties. Today, such newer compounds are the potential targets for the possible novel chemical scaffolds, suitable for mainstream-drug development cascades. Bioactive compounds of Anabaena sp. such as, anatoxins, hassallidins and phycobiliproteins have proven their inherent antibacterial, antifungal, and antineoplastic activities, respectively. Herein, the available details of the biomass production and the inherent phyco-constituents namely, alkaloids, lipids, phenols, peptides, proteins, polysaccharides, terpenoids and cyanotoxins are considered, along with geographical distributions and morphological characteristics of the cyanobacterium. The acquisitions of cyanochemicals in recent years have newly addressed several pharmaceutical aliments, and the understanding of the associated molecular interactions of phycochemicals have been considered, for plausible use in drug developments in future.
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Affiliation(s)
- Chinmayee Priyadarsani Mandhata
- Central Research Laboratory, Institute of Medical Science & SUM Hospital, Siksha O Anusandhan Deemed to be University, Bhubaneswar, 751003, Odisha, India
| | - Ajit Kumar Bishoyi
- Central Research Laboratory, Institute of Medical Science & SUM Hospital, Siksha O Anusandhan Deemed to be University, Bhubaneswar, 751003, Odisha, India
| | - Chita Ranjan Sahoo
- Central Research Laboratory, Institute of Medical Science & SUM Hospital, Siksha O Anusandhan Deemed to be University, Bhubaneswar, 751003, Odisha, India.
| | | | - Rabindra Nath Padhy
- Central Research Laboratory, Institute of Medical Science & SUM Hospital, Siksha O Anusandhan Deemed to be University, Bhubaneswar, 751003, Odisha, India.
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Zhang K, Kries H. Biomimetic engineering of nonribosomal peptide synthesis. Biochem Soc Trans 2023; 51:1521-1532. [PMID: 37409512 DOI: 10.1042/bst20221264] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/07/2023]
Abstract
Nonribosomal peptides (NRPs) have gained attention due to their diverse biological activities and potential applications in medicine and agriculture. The natural diversity of NRPs is a result of evolutionary processes that have occurred over millions of years. Recent studies have shed light on the mechanisms by which nonribosomal peptide synthetases (NRPSs) evolve, including gene duplication, recombination, and horizontal transfer. Mimicking natural evolution could be a useful strategy for engineering NRPSs to produce novel compounds with desired properties. Furthermore, the emergence of antibiotic-resistant bacteria has highlighted the urgent need for new drugs, and NRPs represent a promising avenue for drug discovery. This review discusses the engineering potential of NRPSs in light of their evolutionary history.
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Affiliation(s)
- Kexin Zhang
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena), 07745 Jena, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena), 07745 Jena, Germany
- Organic Chemistry I, University of Bayreuth, 95440 Bayreuth, Germany
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Weisthal Algor S, Sukenik A, Carmeli S. Hydantoanabaenopeptins from Lake Kinneret Microcystis Bloom, Isolation, and Structure Elucidation of the Possible Intermediates in the Anabaenopeptins Biosynthesis. Mar Drugs 2023; 21:401. [PMID: 37504933 PMCID: PMC10381486 DOI: 10.3390/md21070401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023] Open
Abstract
Anabaenopeptins are common metabolites of cyanobacteria. In the course of reisolation of the known aeruginosins KT608A and KT608B for bioassay studies, we noticed the presence of some unknown anabaenopeptins in the extract of a Microcystis cell mass collected during the 2016 spring bloom event in Lake Kinneret, Israel. The 1H NMR spectra of some of these compounds presented a significant difference in the appearance of the ureido bridge protons, and their molecular masses did not match any one of the 152 known anabaenopeptins. Analyses of the 1D and 2D NMR, HRMS, and MS/MS spectra of the new compounds revealed their structures as the hydantoin derivatives of anabaenopeptins A, B, F, and 1[Dht]-anabaenopeptin A and oscillamide Y (1, 2, 3, 6, and 4, respectively) and a new anabaenopeptin, 1[Dht]-anabaenopeptin A (5). The known anabaenopeptins A, B, and F and oscillamide Y (7, 8, 9, and 10, respectively) were present in the extract as well. We propose that 1-4 and 6 are the possible missing intermediates in the previously proposed partial biosynthesis route to the anabaenopeptins. Compounds 1-6 were tested for inhibition of the serine proteases trypsin and chymotrypsin and found inactive at a final concentration of ca. 54 μM.
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Affiliation(s)
- Shira Weisthal Algor
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Assaf Sukenik
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic & Limnological Research Institute, Migdal 49500, Israel
| | - Shmuel Carmeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
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11
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Zhang JW, Wang R, Liang X, Han P, Zheng YL, Li XF, Gao DZ, Liu M, Hou LJ, Dong HP. Novel Gene Clusters for Natural Product Synthesis Are Abundant in the Mangrove Swamp Microbiome. Appl Environ Microbiol 2023; 89:e0010223. [PMID: 37191511 PMCID: PMC10304795 DOI: 10.1128/aem.00102-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023] Open
Abstract
Natural microbial communities produce a diverse array of secondary metabolites with ecologically and biotechnologically relevant activities. Some of them have been used clinically as drugs, and their production pathways have been identified in a few culturable microorganisms. However, since the vast majority of microorganisms in nature have not been cultured, identifying the synthetic pathways of these metabolites and tracking their hosts remain a challenge. The microbial biosynthetic potential of mangrove swamps remains largely unknown. Here, we examined the diversity and novelty of biosynthetic gene clusters in dominant microbial populations in mangrove wetlands by mining 809 newly reconstructed draft genomes and probing the activities and products of these clusters by using metatranscriptomic and metabolomic techniques. A total of 3,740 biosynthetic gene clusters were identified from these genomes, including 1,065 polyketide and nonribosomal peptide gene clusters, 86% of which showed no similarity to known clusters in the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) repository. Of these gene clusters, 59% were harbored by new species or lineages of Desulfobacterota-related phyla and Chloroflexota, whose members are highly abundant in mangrove wetlands and for which few synthetic natural products have been reported. Metatranscriptomics revealed that most of the identified gene clusters were active in field and microcosm samples. Untargeted metabolomics was also used to identify metabolites from the sediment enrichments, and 98% of the mass spectra generated were unrecognizable, further supporting the novelty of these biosynthetic gene clusters. Our study taps into a corner of the microbial metabolite reservoir in mangrove swamps, providing clues for the discovery of new compounds with valuable activities. IMPORTANCE At present, the majority of known clinical drugs originated from cultivated species of a few bacterial lineages. It is vital for the development of new pharmaceuticals to explore the biosynthetic potential of naturally uncultivable microorganisms using new techniques. Based on the large numbers of genomes reconstructed from mangrove wetlands, we identified abundant and diverse biosynthetic gene clusters in previously unsuspected phylogenetic groups. These gene clusters exhibited a variety of organizational architectures, especially for nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS), implying the presence of new compounds with valuable activities in the mangrove swamp microbiome.
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Affiliation(s)
- Jia-Wei Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Ran Wang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Ping Han
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, China
| | - Yan-Ling Zheng
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, China
| | - Xiao-Fei Li
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Deng-Zhou Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Min Liu
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, China
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
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12
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Konkel R, Grabski M, Cegłowska M, Wieczerzak E, Węgrzyn G, Mazur-Marzec H. Anabaenopeptins from Nostoc edaphicum CCNP1411. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:12346. [PMID: 36231642 PMCID: PMC9564503 DOI: 10.3390/ijerph191912346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Cyanobacteria of the Nostoc genus belong to the most prolific sources of bioactive metabolites. In our previous study on Nostoc edaphicum strain CCNP1411, the occurrence of cyanopeptolins and nostocyclopeptides was documented. In the current work, the production of anabaenopeptins (APs) by the strain was studied using genetic and chemical methods. Compatibility between the analysis of the apt gene cluster and the structure of the identified APs was found. Three of the APs, including two new variants, were isolated as pure compounds and tested against four serine proteases and carboxypeptidase A (CPA). The in vitro enzymatic assays showed a typical activity of this class of cyanopeptides, i.e., the most pronounced effects were observed in the case of CPA. The activity of the detected compounds against important metabolic enzymes confirms the pharmaceutical potential of anabaenopeptins.
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Affiliation(s)
- Robert Konkel
- Division of Marine Biotechnology, Institute of Oceanography, University of Gdańsk, M. J. Piłsudskiego 46, PL-81378 Gdynia, Poland
| | - Michał Grabski
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, PL-80308 Gdańsk, Poland
| | - Marta Cegłowska
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, PL-81712 Sopot, Poland
| | - Ewa Wieczerzak
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80308 Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, PL-80308 Gdańsk, Poland
| | - Hanna Mazur-Marzec
- Division of Marine Biotechnology, Institute of Oceanography, University of Gdańsk, M. J. Piłsudskiego 46, PL-81378 Gdynia, Poland
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13
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Phan CS, Mehjabin JJ, Anas ARJ, Hayasaka M, Onoki R, Wang J, Umezawa T, Washio K, Morikawa M, Okino T. Nostosin G and Spiroidesin B from the Cyanobacterium Dolichospermum sp. NIES-1697. JOURNAL OF NATURAL PRODUCTS 2022; 85:2000-2005. [PMID: 35948062 DOI: 10.1021/acs.jnatprod.2c00382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Chemical investigation of the cyanobacterium Dolichospermum sp. NIES-1697 afforded nostosin G (1), a linear tripeptide, spiroidesin B (2), and two known compounds, anabaenopeptins I (3) and J (4). Planar structures and absolute configurations for 1 and 2 were determined by 2D NMR, HRMS, Marfey's methodology, chiral-phase HPLC, and enzymatic degradation. Nostosin G (1) is a unique example of a linear peptide containing three subunits, 4-hydroxyphenyllactic acid (Hpla), homotyrosine (Hty), and argininal, with potent trypsin inhibitory properties. The biosynthetic gene clusters for nostosin G (1) and spiroidesin B (2) were investigated based on the genome sequence of Dolichospermum sp. NIES-1697.
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Krumbholz J, Ishida K, Baunach M, Teikari JE, Rose MM, Sasso S, Hertweck C, Dittmann E. Deciphering Chemical Mediators Regulating Specialized Metabolism in a Symbiotic Cyanobacterium. Angew Chem Int Ed Engl 2022; 61:e202204545. [PMID: 35403785 PMCID: PMC9324945 DOI: 10.1002/anie.202204545] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 11/11/2022]
Abstract
Genomes of cyanobacteria feature a variety of cryptic biosynthetic pathways for complex natural products, but the peculiarities limiting the discovery and exploitation of the metabolic dark matter are not well understood. Here we describe the discovery of two cell density-dependent chemical mediators, nostoclide and nostovalerolactone, in the symbiotic model strain Nostoc punctiforme, and demonstrate their pronounced impact on the regulation of specialized metabolism. Through transcriptional, bioinformatic and labeling studies we assigned two adjacent biosynthetic gene clusters to the biosynthesis of the two polyketide mediators. Our findings provide insight into the orchestration of specialized metabolite production and give lessons for the genomic mining and high-titer production of cyanobacterial bioactive compounds.
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Affiliation(s)
- Julia Krumbholz
- Institute of Biochemistry and BiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Keishi Ishida
- Leibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteBeutenbergstr. 11a07745JenaGermany
| | - Martin Baunach
- Institute of Biochemistry and BiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Jonna E. Teikari
- Institute of Biochemistry and BiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Magdalena M. Rose
- Institute for BiologyDepartment of Plant PhysiologyLeipzig UniversityJohannisallee 21–2304103LeipzigGermany
| | - Severin Sasso
- Institute for BiologyDepartment of Plant PhysiologyLeipzig UniversityJohannisallee 21–2304103LeipzigGermany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteBeutenbergstr. 11a07745JenaGermany
- Institute of MicrobiologyFaculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
| | - Elke Dittmann
- Institute of Biochemistry and BiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
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15
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Kaari M, Manikkam R, Baskaran A. Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:448-467. [PMID: 35394575 DOI: 10.1007/s10126-022-10118-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Marine microbes genetically evolved to survive varying salinity, temperature, pH, and other stress factors by producing different bioactive metabolites. These microbial secondary metabolites (SMs) are novel, have high potential, and could be used as lead molecule. Genome sequencing of microbes revealed that they have the capability to produce numerous novel bioactive metabolites than observed under standard in vitro culture conditions. Microbial genome has specific regions responsible for SM assembly, termed biosynthetic gene clusters (BGCs), possessing all the necessary genes to encode different enzymes required to generate SM. In order to augment the microbial chemo diversity and to activate these gene clusters, various tools and techniques are developed. Metagenomics with functional gene expression studies aids in classifying novel peptides and enzymes and also in understanding the biosynthetic pathways. Genome shuffling is a high-throughput screening approach to improve the development of SMs by incorporating genomic recombination. Transcriptionally silent or lower level BGCs can be triggered by artificially knocking promoter of target BGC. Additionally, bioinformatic tools like antiSMASH, ClustScan, NAPDOS, and ClusterFinder are effective in identifying BGCs of existing class for annotation in genomes. This review summarizes the significance of BGCs and the different approaches for detecting and elucidating BGCs from marine microbes.
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Affiliation(s)
- Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India.
| | - Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
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16
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Krumbholz J, Ishida K, Baunach M, Teikari JE, Rose MM, Sasso S, Hertweck C, Dittmann E. Entschlüsselung chemischer Mediatoren zur Regulierung des spezialisierten Stoffwechsels in einem symbiotischen Cyanobakterium. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Julia Krumbholz
- Institut für Biochemie und Biologie Universität Potsdam Karl-Liebknecht-Str. 24/25 14476 Potsdam-Golm Deutschland
| | - Keishi Ishida
- Leibniz Institut für Naturstoff-Forschung und Infektionsbiologie Hans Knöll Institute Beutenbergstr. 11a 07745 Jena Deutschland
| | - Martin Baunach
- Institut für Biochemie und Biologie Universität Potsdam Karl-Liebknecht-Str. 24/25 14476 Potsdam-Golm Deutschland
| | - Jonna E. Teikari
- Institut für Biochemie und Biologie Universität Potsdam Karl-Liebknecht-Str. 24/25 14476 Potsdam-Golm Deutschland
| | - Magdalena M. Rose
- Institut für Biologie AG Pflanzenphysiologie Universität Leipzig Johannisallee 21–23 04103 Leipzig Deutschland
| | - Severin Sasso
- Institut für Biologie AG Pflanzenphysiologie Universität Leipzig Johannisallee 21–23 04103 Leipzig Deutschland
| | - Christian Hertweck
- Leibniz Institut für Naturstoff-Forschung und Infektionsbiologie Hans Knöll Institute Beutenbergstr. 11a 07745 Jena Deutschland
- Institut für Mikrobiologie Fakultät für Biowissenschaften Friedrich-Schiller-Universität Jena 07743 Jena Deutschland
| | - Elke Dittmann
- Institut für Biochemie und Biologie Universität Potsdam Karl-Liebknecht-Str. 24/25 14476 Potsdam-Golm Deutschland
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17
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Hendrix H, Zimmermann-Kogadeeva M, Zimmermann M, Sauer U, De Smet J, Muchez L, Lissens M, Staes I, Voet M, Wagemans J, Ceyssens PJ, Noben JP, Aertsen A, Lavigne R. Metabolic reprogramming of Pseudomonas aeruginosa by phage-based quorum sensing modulation. Cell Rep 2022; 38:110372. [PMID: 35172131 DOI: 10.1016/j.celrep.2022.110372] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/29/2021] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
The Pseudomonas quinolone signal (PQS) is a multifunctional quorum sensing molecule of key importance to P. aeruginosa. Here, we report that the lytic Pseudomonas bacterial virus LUZ19 targets this population density-dependent signaling system by expressing quorum sensing targeting protein (Qst) early during infection. We demonstrate that Qst interacts with PqsD, a key host quinolone signal biosynthesis pathway enzyme, resulting in decreased levels of PQS and its precursor 2-heptyl-4(1H)-quinolone. The lack of a functional PqsD enzyme impairs LUZ19 infection but is restored by external supplementation of 2-heptyl-4(1H)-quinolone, suggesting that LUZ19 exploits the PQS system for successful infection. We establish a broad functional interaction network of Qst, which includes enzymes of cofactor biosynthesis pathways (CoaC/ThiD) and a non-ribosomal peptide synthetase pathway (PA1217). Qst therefore represents an exquisite example of intricate reprogramming of the bacterium by a phage, which may be further exploited as tool to combat antibiotic resistant bacterial pathogens.
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Affiliation(s)
- Hanne Hendrix
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | | | - Michael Zimmermann
- Institute of Molecular Systems Biology, ETH Zurich, 8092 Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, 8092 Zürich, Switzerland
| | - Jeroen De Smet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Laurens Muchez
- Centre for Surface Chemistry and Catalysis, Department of Microbial and Molecular Systems, KU Leuven, 3001 Heverlee, Belgium
| | - Maries Lissens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Ines Staes
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, KU Leuven, 3001 Heverlee, Belgium
| | - Marleen Voet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Pieter-Jan Ceyssens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, School of Life Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, KU Leuven, 3001 Heverlee, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium.
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18
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Zervou SK, Kaloudis T, Gkelis S, Hiskia A, Mazur-Marzec H. Anabaenopeptins from Cyanobacteria in Freshwater Bodies of Greece. Toxins (Basel) 2021; 14:4. [PMID: 35050981 PMCID: PMC8781842 DOI: 10.3390/toxins14010004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/06/2021] [Accepted: 12/15/2021] [Indexed: 12/27/2022] Open
Abstract
Cyanobacteria are photosynthetic microorganisms that are able to produce a large number of secondary metabolites. In freshwaters, under favorable conditions, they can rapidly multiply, forming blooms, and can release their toxic/bioactive metabolites in water. Among them, anabaenopeptins (APs) are a less studied class of cyclic bioactive cyanopeptides. The occurrence and structural variety of APs in cyanobacterial blooms and cultured strains from Greek freshwaters were investigated. Cyanobacterial extracts were analyzed with LC-qTRAP MS/MS using information-dependent acquisition in enhanced ion product mode in order to obtain the fragmentation mass spectra of APs. Thirteen APs were detected, and their possible structures were annotated based on the elucidation of fragmentation spectra, including three novel ones. APs were present in the majority of bloom samples (91%) collected from nine Greek lakes during different time periods. A large variety of APs was observed, with up to eight congeners co-occurring in the same sample. AP F (87%), Oscillamide Y (87%) and AP B (65%) were the most frequently detected congeners. Thirty cyanobacterial strain cultures were also analyzed. APs were only detected in one strain (Microcystis ichtyoblabe). The results contribute to a better understanding of APs produced by freshwater cyanobacteria and expand the range of structurally characterized APs.
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Affiliation(s)
- Sevasti-Kiriaki Zervou
- Laboratory of Photo-Catalytic Processes and Environmental Chemistry, Institute of Nanoscience & Nanotechnology, National Centre for Scientific Research “Demokritos”, Patriarchou Grigoriou E & 27 Neapoleos Str., 15310 Athens, Greece; (T.K.); (A.H.)
| | - Triantafyllos Kaloudis
- Laboratory of Photo-Catalytic Processes and Environmental Chemistry, Institute of Nanoscience & Nanotechnology, National Centre for Scientific Research “Demokritos”, Patriarchou Grigoriou E & 27 Neapoleos Str., 15310 Athens, Greece; (T.K.); (A.H.)
| | - Spyros Gkelis
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Anastasia Hiskia
- Laboratory of Photo-Catalytic Processes and Environmental Chemistry, Institute of Nanoscience & Nanotechnology, National Centre for Scientific Research “Demokritos”, Patriarchou Grigoriou E & 27 Neapoleos Str., 15310 Athens, Greece; (T.K.); (A.H.)
| | - Hanna Mazur-Marzec
- Division of Marine Biotechnology, University of Gdansk, Al. Marszałka Piłsudskiego 46, 81-378 Gdynia, Poland;
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Abstract
Cyanobacteria constitute an interesting group of photosynthetic microorganisms due to their morphological and genetic diversity that is related to their extremely long evolution process, which created the need for them to adapt to immensely heterogeneous environmental conditions. Cyanobacteria grow in salt and fresh waters as well as on the surface of soils and rocks. The diverse cell structure is characterized by the fact that they occur in many morphological forms, from small single cells through to larger ones as well as branches, threads, or spirals. Taking into account the presence of cyanobacteria in virtually all possible conditions and places on Earth, cyanobacteria represent an unexplored potential that is worth investigating. This review presents the possibilities of using algae in chosen areas of biotechnology: e.g., as biocatalysts or in industries such as the pharmaceutical industry. It covers the characteristics of secondary metabolites along with their division and the potential of using them as sources of effective drugs for many diseases. It presents an overview of the possibilities of using cyanobacteria in biotransformation processes. These processes are of great importance in the case of, for example, the neutralization of municipal, industrial, or chemical waste, the amount of which is constantly growing every year, and they are also an easier and cheaper path to obtain chemical compounds.
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20
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Nandagopal P, Steven AN, Chan LW, Rahmat Z, Jamaluddin H, Mohd Noh NI. Bioactive Metabolites Produced by Cyanobacteria for Growth Adaptation and Their Pharmacological Properties. BIOLOGY 2021; 10:1061. [PMID: 34681158 PMCID: PMC8533319 DOI: 10.3390/biology10101061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/10/2021] [Accepted: 10/14/2021] [Indexed: 02/08/2023]
Abstract
Cyanobacteria are the most abundant oxygenic photosynthetic organisms inhabiting various ecosystems on earth. As with all other photosynthetic organisms, cyanobacteria release oxygen as a byproduct during photosynthesis. In fact, some cyanobacterial species are involved in the global nitrogen cycles by fixing atmospheric nitrogen. Environmental factors influence the dynamic, physiological characteristics, and metabolic profiles of cyanobacteria, which results in their great adaptation ability to survive in diverse ecosystems. The evolution of these primitive bacteria resulted from the unique settings of photosynthetic machineries and the production of bioactive compounds. Specifically, bioactive compounds play roles as regulators to provide protection against extrinsic factors and act as intracellular signaling molecules to promote colonization. In addition to the roles of bioactive metabolites as indole alkaloids, terpenoids, mycosporine-like amino acids, non-ribosomal peptides, polyketides, ribosomal peptides, phenolic acid, flavonoids, vitamins, and antimetabolites for cyanobacterial survival in numerous habitats, which is the focus of this review, the bioactivities of these compounds for the treatment of various diseases are also discussed.
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Affiliation(s)
- Pavitra Nandagopal
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (P.N.); (L.-W.C.); (Z.R.); (H.J.)
| | - Anthony Nyangson Steven
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Malaysia;
| | - Liong-Wai Chan
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (P.N.); (L.-W.C.); (Z.R.); (H.J.)
| | - Zaidah Rahmat
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (P.N.); (L.-W.C.); (Z.R.); (H.J.)
- Institute of Bioproduct Development, Universiti Teknologi Malaysia, Skudai 81310, Malaysia
| | - Haryati Jamaluddin
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (P.N.); (L.-W.C.); (Z.R.); (H.J.)
| | - Nur Izzati Mohd Noh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (P.N.); (L.-W.C.); (Z.R.); (H.J.)
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21
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Anabaenopeptins: What We Know So Far. Toxins (Basel) 2021; 13:toxins13080522. [PMID: 34437393 PMCID: PMC8402340 DOI: 10.3390/toxins13080522] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
Cyanobacteria are microorganisms with photosynthetic mechanisms capable of colonizing several distinct environments worldwide. They can produce a vast spectrum of bioactive compounds with different properties, resulting in an improved adaptative capacity. Their richness in secondary metabolites is related to their unique and diverse metabolic apparatus, such as Non-Ribosomal Peptide Synthetases (NRPSs). One important class of peptides produced by the non-ribosomal pathway is anabaenopeptins. These cyclic hexapeptides demonstrated inhibitory activity towards phosphatases and proteases, which could be related to their toxicity and adaptiveness against zooplankters and crustaceans. Thus, this review aims to identify key features related to anabaenopeptins, including the diversity of their structure, occurrence, the biosynthetic steps for their production, ecological roles, and biotechnological applications.
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Baunach M, Chowdhury S, Stallforth P, Dittmann E. The Landscape of Recombination Events That Create Nonribosomal Peptide Diversity. Mol Biol Evol 2021; 38:2116-2130. [PMID: 33480992 PMCID: PMC8097286 DOI: 10.1093/molbev/msab015] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nonribosomal peptides (NRP) are crucial molecular mediators in microbial ecology and provide indispensable drugs. Nevertheless, the evolution of the flexible biosynthetic machineries that correlates with the stunning structural diversity of NRPs is poorly understood. Here, we show that recombination is a key driver in the evolution of bacterial NRP synthetase (NRPS) genes across distant bacterial phyla, which has guided structural diversification in a plethora of NRP families by extensive mixing and matching of biosynthesis genes. The systematic dissection of a large number of individual recombination events did not only unveil a striking plurality in the nature and origin of the exchange units but allowed the deduction of overarching principles that enable the efficient exchange of adenylation (A) domain substrates while keeping the functionality of the dynamic multienzyme complexes. In the majority of cases, recombination events have targeted variable portions of the Acore domains, yet domain interfaces and the flexible Asub domain remained untapped. Our results strongly contradict the widespread assumption that adenylation and condensation (C) domains coevolve and significantly challenge the attributed role of C domains as stringent selectivity filter during NRP synthesis. Moreover, they teach valuable lessons on the choice of natural exchange units in the evolution of NRPS diversity, which may guide future engineering approaches.
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Affiliation(s)
- Martin Baunach
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Somak Chowdhury
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Jena, Germany
| | - Pierre Stallforth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Jena, Germany
| | - Elke Dittmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
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Jacinavicius FR, Geraldes V, Crnkovic CM, Delbaje E, Fiore MF, Pinto E. Effect of ultraviolet radiation on the metabolomic profiles of potentially toxic cyanobacteria. FEMS Microbiol Ecol 2021; 97:6006873. [PMID: 33242088 DOI: 10.1093/femsec/fiaa243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/24/2020] [Indexed: 11/13/2022] Open
Abstract
Interactions between climate change and ultraviolet radiation (UVR) have a substantial impact on aquatic ecosystems, especially on photosynthetic organisms. To counteract the damaging effects of UVR, cyanobacteria developed adaptive strategies such as the biosynthesis of secondary metabolites. This study aimed to evaluate the effects of UVR on the metabolomic profiles of potentially toxic cyanobacteria. Twelve strains were irradiated with ultraviolet A and ultraviolet B radiation and parabolic aluminized reflector lamps for 3 days, followed by liquid chromatography-tandem mass spectometry (LC-MS/MS) analysis to assess changes in metabolomic profiles. Matrices were used to generate principal component analysis biplots, and molecular networks were obtained using the Global Natural Products platform. Most strains showed significant changes in their metabolomic profiles after UVR exposure. On average, 7% of MS features were shown to be exclusive to metabolomic profiles before UVR exposure, while 9% were unique to metabolomic profiles after UVR exposure. The identified compounds included aeruginosins, spumigins, cyanopeptolins, microginins, namalides, pseudospumigins, anabaenopeptins, mycosporine-like amino acids, nodularins and microcystins. Data showed that cyanobacteria display broad metabolic plasticity upon UVR exposure, including the synthesis and differential expression of a variety of secondary metabolites. This could result in a competitive advantage, supporting cyanobacterial blooms under various UVR light exposures.
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Affiliation(s)
| | - Vanessa Geraldes
- University of São Paulo, School of Pharmaceutical Sciences, São Paulo-SP, Brazil
| | - Camila M Crnkovic
- University of São Paulo, School of Pharmaceutical Sciences, São Paulo-SP, Brazil
| | - Endrews Delbaje
- University of São Paulo, Centre for Nuclear Energy in Agriculture, Piracicaba-SP, Brazil
| | - Marli F Fiore
- University of São Paulo, Centre for Nuclear Energy in Agriculture, Piracicaba-SP, Brazil
| | - Ernani Pinto
- University of São Paulo, School of Pharmaceutical Sciences, São Paulo-SP, Brazil.,University of São Paulo, Centre for Nuclear Energy in Agriculture, Piracicaba-SP, Brazil
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Dreher TW, Davis EW, Mueller RS, Otten TG. Comparative genomics of the ADA clade within the Nostocales. HARMFUL ALGAE 2021; 104:102037. [PMID: 34023075 DOI: 10.1016/j.hal.2021.102037] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/14/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
The ADA clade of Nostocales cyanobacteria, a group that is prominent in current harmful algal bloom events, now includes over 40 genome sequences with the recent addition of sixteen novel sequenced genomes (Dreher et al., Harmful Algae, 2021). Fourteen genomes are complete (closed), enabling highly detailed assessments of gene content and genome architecture. ADA genomes contain 5 rRNA operons, genes expected to support a photoautotrophic and diazotrophic lifestyle, and a varied array of genes for the synthesis of bioactive secondary metabolites. Genes for the production of the taste-and-odor compound geosmin and the four major classes of cyanotoxins - anatoxin-a, cylindrospermopsin, microcystin and saxitoxin - are represented in members of the ADA clade. Notably, the gene array for the synthesis of cylindrospermopsin by Dolichospermum sp. DET69 was located on a plasmid, raising the possibility of facile horizontal transmission. However, genes supporting independent conjugative transfer of this plasmid are lacking. Further, analysis of genomic loci containing this and other cyanotoxin gene arrays shows evidence that these arrays have long-term stability and do not appear to be genomic islands easily capable of horizontal transmission to other cells. There is considerable diversity in the gene complements of individual ADA genomes, including the variable presence of physiologically important genes: genomes in three species-level subclades lack the gas vesicle genes that facilitate a planktonic lifestyle, and, surprisingly, the genome of Cuspidothrix issatschenkoi CHARLIE-1, a reported diazotroph, lacks the genes for nitrogen fixation. Notably, phylogenetically related genomes possess limited synteny, indicating a prominent role for chromosome rearrangements during ADA strain evolution. The genomes contain abundant insertion sequences and repetitive transposase genes, which could be the main drivers of genome rearrangement through active transposition and homologous recombination. No prophages were found, and no evidence of viral infection was observed in the bloom population samples from which the genomes discussed here were derived. Phages thus seem to have a limited influence on ADA evolution.
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Affiliation(s)
- Theo W Dreher
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331 USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331 USA.
| | - Edward W Davis
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331 USA
| | - Ryan S Mueller
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Timothy G Otten
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331 USA.
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25
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Sulheim S, Fossheim FA, Wentzel A, Almaas E. Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters. BMC Bioinformatics 2021; 22:81. [PMID: 33622234 PMCID: PMC7901079 DOI: 10.1186/s12859-021-03985-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/18/2021] [Indexed: 12/17/2022] Open
Abstract
Background A wide range of bioactive compounds is produced by enzymes and enzymatic complexes encoded in biosynthetic gene clusters (BGCs). These BGCs can be identified and functionally annotated based on their DNA sequence. Candidates for further research and development may be prioritized based on properties such as their functional annotation, (dis)similarity to known BGCs, and bioactivity assays. Production of the target compound in the native strain is often not achievable, rendering heterologous expression in an optimized host strain as a promising alternative. Genome-scale metabolic models are frequently used to guide strain development, but large-scale incorporation and testing of heterologous production of complex natural products in this framework is hampered by the amount of manual work required to translate annotated BGCs to metabolic pathways. To this end, we have developed a pipeline for an automated reconstruction of BGC associated metabolic pathways responsible for the synthesis of non-ribosomal peptides and polyketides, two of the dominant classes of bioactive compounds. Results The developed pipeline correctly predicts 72.8% of the metabolic reactions in a detailed evaluation of 8 different BGCs comprising 228 functional domains. By introducing the reconstructed pathways into a genome-scale metabolic model we demonstrate that this level of accuracy is sufficient to make reliable in silico predictions with respect to production rate and gene knockout targets. Furthermore, we apply the pipeline to a large BGC database and reconstruct 943 metabolic pathways. We identify 17 enzymatic reactions using high-throughput assessment of potential knockout targets for increasing the production of any of the associated compounds. However, the targets only provide a relative increase of up to 6% compared to wild-type production rates. Conclusion With this pipeline we pave the way for an extended use of genome-scale metabolic models in strain design of heterologous expression hosts. In this context, we identified generic knockout targets for the increased production of heterologous compounds. However, as the predicted increase is minor for any of the single-reaction knockout targets, these results indicate that more sophisticated strain-engineering strategies are necessary for the development of efficient BGC expression hosts.
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Affiliation(s)
- Snorre Sulheim
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Sem Sælands vei 8, 7034, Trondheim, Norway. .,Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands vei 3, 7034, Trondheim, Norway.
| | - Fredrik A Fossheim
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Sem Sælands vei 8, 7034, Trondheim, Norway
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands vei 3, 7034, Trondheim, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Sem Sælands vei 8, 7034, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, Håkon Jarls gate 11, 7030, Trondheim, Norway
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26
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Porzani SJ, Lima ST, Metcalf JS, Nowruzi B. In Vivo and In Vitro Toxicity Testing of Cyanobacterial Toxins: A Mini-Review. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 258:109-150. [PMID: 34622370 DOI: 10.1007/398_2021_74] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Harmful cyanobacterial blooms are increasing and becoming a worldwide concern as many bloom-forming cyanobacterial species can produce toxic metabolites named cyanotoxins. These include microcystins, saxitoxins, anatoxins, nodularins, and cylindrospermopsins, which can adversely affect humans, animals, and the environment. Different methods to assess these classes of compounds in vitro and in vivo include biological, biochemical, molecular, and physicochemical techniques. Furthermore, toxic effects not attributable to known cyanotoxins can be observed when assessing bloom material. In order to determine exposures to cyanotoxins and to monitor compliance with drinking and bathing water guidelines, it is necessary to have reliable and effective methods for the analysis of these compounds. Many relatively simple low-cost methods can be employed to rapidly evaluate the potential hazard. The main objective of this mini-review is to describe the assessment of toxic cyanobacterial samples using in vitro and in vivo bioassays. Newly emerging cyanotoxins, the toxicity of analogs, or the interaction of cyanobacteria and cyanotoxins with other toxicants, among others, still requires bioassay assessment. This review focuses on some biological and biochemical assays (MTT assay, Immunohistochemistry, Micronucleus Assay, Artemia salina assay, Daphnia magna test, Radionuclide recovery, Neutral red cytotoxicity and Comet assay, Enzyme-Linked Immunosorbent Assay (ELISA), Annexin V-FITC assay and Protein Phosphatase Inhibition Assay (PPIA)) for the detection and measurement of cyanotoxins including microcystins, cylindrospermopsins, anatoxin-a, saxitoxins, and nodularins. Although most bioassay analyses often confirm the presence of cyanotoxins at low concentrations, such bioassays can be used to determine whether some strains or blooms of cyanobacteria may produce other, as yet unknown toxic metabolites. This review also aims to identify research needs and data gaps concerning the toxicity assessment of cyanobacteria.
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Affiliation(s)
- Samaneh J Porzani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Stella T Lima
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | | | - Bahareh Nowruzi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
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Shimura Y, Fujisawa T, Hirose Y, Misawa N, Kanesaki Y, Nakamura Y, Kawachi M. Complete sequence and structure of the genome of the harmful algal bloom-forming cyanobacterium Planktothrix agardhii NIES-204 T and detailed analysis of secondary metabolite gene clusters. HARMFUL ALGAE 2021; 101:101942. [PMID: 33526179 DOI: 10.1016/j.hal.2020.101942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Planktothrix species are distributed worldwide, and these prevalent cyanobacteria occasionally form potentially devastating toxic blooms. Given the ecological and taxonomic importance of Planktothrix agardhii as a bloom species, we set out to determine the complete genome sequence of the type strain Planktothrix agardhii NIES-204. Remarkably, we found that the 5S ribosomal RNA genes are not adjacent to the 16S and 23S ribosomal RNA genes. The genomic structure of P. agardhii NIES-204 is highly similar to that of another P. agardhii strain isolated from a geographically distant site, although they differ distinctly by a large inversion. We identified numerous gene clusters that encode the components of the metabolic pathways that generate secondary metabolites. We found that the aeruginosin biosynthetic gene cluster was more similar to that of another toxic bloom-forming cyanobacterium Microcystis aeruginosa than to that of other strains of Planktothrix, suggesting horizontal gene transfer. Prenyltransferases encoded in the prenylagaramide gene cluster of Planktothrix strains were classified into two phylogenetically distinct types, suggesting a functional difference. In addition to the secondary metabolite gene clusters, we identified genes for inorganic nitrogen and phosphate uptake components and gas vesicles. Our findings contribute to further understanding of the ecologically important genus Planktothrix.
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Affiliation(s)
- Yohei Shimura
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan.
| | - Takatomo Fujisawa
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Hibarigaoka 1-1, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Naomi Misawa
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Hibarigaoka 1-1, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
| | - Yasukazu Nakamura
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
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28
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Nowruzi B, Porzani SJ. Toxic compounds produced by cyanobacteria belonging to several species of the order Nostocales: A review. J Appl Toxicol 2020; 41:510-548. [PMID: 33289164 DOI: 10.1002/jat.4088] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/12/2022]
Abstract
Cyanobacteria are well recognised as producers of a wide range of natural compounds that are in turn recognised as toxins that have potential and useful applications in the future as pharmaceutical agents. The order Nostocales, which is largely overlooked in this regard, has become increasingly recognised as a source of toxin producers including Anabaena, Nostoc, Hapalosiphon, Fischerella, Anabaenopsis, Aphanizomenon, Gloeotrichia, Cylindrospermopsis, Scytonema, Raphidiopsis, Cuspidothrix, Nodularia, Stigonema, Calothrix, Cylindrospermum and Desmonostoc species. The toxin compounds (i.e., microcystins, nodularin, anatoxins, ambiguines, fischerindoles and welwitindolinones) and metabolites are about to have a destructive effect on both inland and aquatic environment aspects. The present review gives an overview of the various toxins that are extracted by the order Nostocales. The current research suggests that these compounds that are produced by cyanobacterial species have promising future considerations as potentially harmful algae and as promising leads for drug discovery.
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Affiliation(s)
- Bahareh Nowruzi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Samaneh Jafari Porzani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
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29
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Liu Z, Lei D, Qiao B, Li S, Qiao J, Zhao GR. Integrative Biosynthetic Gene Cluster Mining to Optimize a Metabolic Pathway to Efficiently Produce l-Homophenylalanine in Escherichia coli. ACS Synth Biol 2020; 9:2943-2954. [PMID: 33078922 DOI: 10.1021/acssynbio.0c00363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mining biosynthetic genes for the exploration of hybrid metabolic pathways is a promising approach in heterologous production of natural and unnatural products. Here, we developed an integrative biosynthetic gene cluster (BGC) mining strategy to engineer the biosynthesis of l-homophenylalanine (l-Hph), an important intermediate for the synthesis of angiotensin-converting enzyme inhibitors. We assembled the putative l-Hph BGCs and integrated phylogenetic analysis with target metabolite abundance mapping to prioritize candidate BGCs. To obtain an effective l-Hph pathway, various combinations of candidate genes from different species were screened in an iterative design-build-test stepwise manner. After the pathway was strength balanced and the metabolic flux was enhanced, engineered Escherichia coli produced 1.41 g/L of l-Hph from glucose in feeding shake-flask fermentation. Our cluster mining strategy enabled optimization of the target metabolic pathway, and it would be promising for production of other valuable products in the postgenomic era.
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Affiliation(s)
- Zhenning Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Dengwei Lei
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Bin Qiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Shilin Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Jianjun Qiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Guang-Rong Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
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30
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Heinilä LMP, Fewer DP, Jokela JK, Wahlsten M, Jortikka A, Sivonen K. Shared PKS Module in Biosynthesis of Synergistic Laxaphycins. Front Microbiol 2020; 11:578878. [PMID: 33042096 PMCID: PMC7524897 DOI: 10.3389/fmicb.2020.578878] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/17/2020] [Indexed: 12/13/2022] Open
Abstract
Cyanobacteria produce a wide range of lipopeptides that exhibit potent membrane-disrupting activities. Laxaphycins consist of two families of structurally distinct macrocyclic lipopeptides that act in a synergistic manner to produce antifungal and antiproliferative activities. Laxaphycins are produced by range of cyanobacteria but their biosynthetic origins remain unclear. Here, we identified the biosynthetic pathways responsible for the biosynthesis of the laxaphycins produced by Scytonema hofmannii PCC 7110. We show that these laxaphycins, called scytocyclamides, are produced by this cyanobacterium and are encoded in a single biosynthetic gene cluster with shared polyketide synthase enzymes initiating two distinct non-ribosomal peptide synthetase pathways. The unusual mechanism of shared enzymes synthesizing two distinct types of products may aid future research in identifying and expressing natural product biosynthetic pathways and in expanding the known biosynthetic logic of this important family of natural products.
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Affiliation(s)
| | - David P Fewer
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Jouni Kalevi Jokela
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Matti Wahlsten
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Anna Jortikka
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Kaarina Sivonen
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
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31
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Fidor A, Grabski M, Gawor J, Gromadka R, Węgrzyn G, Mazur-Marzec H. Nostoc edaphicum CCNP1411 from the Baltic Sea-A New Producer of Nostocyclopeptides. Mar Drugs 2020; 18:E442. [PMID: 32858999 PMCID: PMC7551626 DOI: 10.3390/md18090442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 12/17/2022] Open
Abstract
Nostocyclopeptides (Ncps) constitute a small class of nonribosomal peptides, exclusively produced by cyanobacteria of the genus Nostoc. The peptides inhibit the organic anion transporters, OATP1B3 and OATP1B1, and prevent the transport of the toxic microcystins and nodularin into hepatocytes. So far, only three structural analogues, Ncp-A1, Ncp-A2 and Ncp-M1, and their linear forms were identified in Nostoc strains as naturally produced cyanometabolites. In the current work, the whole genome sequence of the new Ncps producer, N. edaphicum CCNP1411 from the Baltic Sea, has been determined. The genome consists of the circular chromosome (7,733,505 bps) and five circular plasmids (from 44.5 kb to 264.8 kb). The nostocyclopeptide biosynthetic gene cluster (located between positions 7,609,981-7,643,289 bps of the chromosome) has been identified and characterized in silico. The LC-MS/MS analyzes of N. edaphicum CCNP1411 cell extracts prepared in aqueous methanol revealed several products of the genes. Besides the known peptides, Ncp-A1 and Ncp-A2, six other compounds putatively characterized as new noctocyclopeptide analogues were detected. This includes Ncp-E1 and E2 and their linear forms (Ncp-E1-L and E2-L), a cyclic Ncp-E3 and a linear Ncp-E4-L. Regardless of the extraction conditions, the cell contents of the linear nostocyclopeptides were found to be higher than the cyclic ones, suggesting a slow rate of the macrocyclization process.
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Affiliation(s)
- Anna Fidor
- Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Marszałka J. Piłsudskiego 46, PL-81378 Gdynia, Poland;
| | - Michał Grabski
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (G.W.)
| | - Jan Gawor
- DNA Sequencing and Oligonucleotide Synthesis Laboratory, Polish Academy of Sciences, Institute of Biochemistry and Biophysics, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Robert Gromadka
- DNA Sequencing and Oligonucleotide Synthesis Laboratory, Polish Academy of Sciences, Institute of Biochemistry and Biophysics, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (G.W.)
| | - Hanna Mazur-Marzec
- Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Marszałka J. Piłsudskiego 46, PL-81378 Gdynia, Poland;
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Discovery of Unusual Cyanobacterial Tryptophan-Containing Anabaenopeptins by MS/MS-Based Molecular Networking. Molecules 2020; 25:molecules25173786. [PMID: 32825321 PMCID: PMC7503407 DOI: 10.3390/molecules25173786] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/11/2020] [Accepted: 08/19/2020] [Indexed: 12/27/2022] Open
Abstract
Heterocytous cyanobacteria are among the most prolific sources of bioactive secondary metabolites, including anabaenopeptins (APTs). A terrestrial filamentous Brasilonema sp. CT11 collected in Costa Rica bamboo forest as a black mat, was studied using a multidisciplinary approach: genome mining and HPLC-HRMS/MS coupled with bioinformatic analyses. Herein, we report the nearly complete genome consisting of 8.79 Mbp with a GC content of 42.4%. Moreover, we report on three novel tryptophan-containing APTs; anabaenopeptin 788 (1), anabaenopeptin 802 (2), and anabaenopeptin 816 (3). Furthermore, the structure of two homologues, i.e., anabaenopeptin 802 (2a) and anabaenopeptin 802 (2b), was determined by spectroscopic analysis (NMR and MS). Both compounds were shown to exert weak to moderate antiproliferative activity against HeLa cell lines. This study also provides the unique and diverse potential of biosynthetic gene clusters and an assessment of the predicted chemical space yet to be discovered from this genus.
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May DS, Crnkovic CM, Krunic A, Wilson TA, Fuchs JR, Orjala JE. 15N Stable Isotope Labeling and Comparative Metabolomics Facilitates Genome Mining in Cultured Cyanobacteria. ACS Chem Biol 2020; 15:758-765. [PMID: 32083834 DOI: 10.1021/acschembio.9b00993] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As genome mining becomes a more widely used approach to identify bacterial natural products, the challenge of matching biosynthetic gene clusters to their cognate secondary metabolites has become more apparent. Bioinformatic platforms such as AntiSMASH have made great progress in predicting chemical structures from genetic information, however the predicted structures are often incomplete. This complicates identifying the predicted compounds by mass spectrometry. Secondary metabolites produced by cyanobacteria represent a unique opportunity for bridging this gap. Cultured cyanobacteria incorporate inorganic nitrogen provided in chemically defined media into all nitrogen-containing secondary metabolites. Thus, stable isotope labeling with 15N labeled nitrate and subsequent comparative metabolomics can be used to match biosynthetic gene clusters to their cognate compounds in cell extracts. Analysis of the sequenced genome of Nostoc sp. UIC 10630 identified six biosynthetic gene clusters predicted to encode the production of a secondary metabolite with at least one nitrogen atom. Comparative metabolomic analysis of the 15N labeled and unlabeled cell extracts revealed four nitrogen containing compounds that contained the same number of nitrogen atoms as were predicted in the biosynthetic gene clusters. Two of the four compounds were new secondary metabolites, and their structures were elucidated by NMR, HRESIMS, and MS/MS.
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Affiliation(s)
- Daniel S. May
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Camila M. Crnkovic
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Federal District 70040-020, Brazil
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Aleksej Krunic
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Tyler A. Wilson
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - James R. Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jimmy E. Orjala
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
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Popin RV, Delbaje E, de Abreu VAC, Rigonato J, Dörr FA, Pinto E, Sivonen K, Fiore MF. Genomic and Metabolomic Analyses of Natural Products in Nodularia spumigena Isolated from a Shrimp Culture Pond. Toxins (Basel) 2020; 12:toxins12030141. [PMID: 32106513 PMCID: PMC7150779 DOI: 10.3390/toxins12030141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/13/2020] [Accepted: 02/21/2020] [Indexed: 11/16/2022] Open
Abstract
The bloom-forming cyanobacterium Nodularia spumigena CENA596 encodes the biosynthetic gene clusters (BGCs) of the known natural products nodularins, spumigins, anabaenopeptins/namalides, aeruginosins, mycosporin-like amino acids, and scytonemin, along with the terpenoid geosmin. Targeted metabolomics confirmed the production of these metabolic compounds, except for the alkaloid scytonemin. Genome mining of N. spumigena CENA596 and its three closely related Nodularia strains—two planktonic strains from the Baltic Sea and one benthic strain from Japanese marine sediment—revealed that the number of BGCs in planktonic strains was higher than in benthic one. Geosmin—a volatile compound with unpleasant taste and odor—was unique to the Brazilian strain CENA596. Automatic annotation of the genomes using subsystems technology revealed a related number of coding sequences and functional roles. Orthologs from the Nodularia genomes are involved in the primary and secondary metabolisms. Phylogenomic analysis of N. spumigena CENA596 based on 120 conserved protein sequences positioned this strain close to the Baltic Nodularia. Phylogeny of the 16S rRNA genes separated the Brazilian CENA596 strain from those of the Baltic Sea, despite their high sequence identities (99% identity, 100% coverage). The comparative analysis among planktic Nodularia strains showed that their genomes were considerably similar despite their geographically distant origin.
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Affiliation(s)
- Rafael Vicentini Popin
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland;
| | - Endrews Delbaje
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
| | - Vinicius Augusto Carvalho de Abreu
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Institute of Exact and Natural Sciences, Federal University of Pará, Rua Augusto Corrêa 1, Belém 66075-10, Pará, Brazil
| | - Janaina Rigonato
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
| | - Felipe Augusto Dörr
- Faculty of Pharmaceutical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, São Paulo 05508-000, São Paulo, Brazil;
| | - Ernani Pinto
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Faculty of Pharmaceutical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, São Paulo 05508-000, São Paulo, Brazil;
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland;
| | - Marli Fatima Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Correspondence:
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Bioactive Peptides Produced by Cyanobacteria of the Genus Nostoc: A Review. Mar Drugs 2019; 17:md17100561. [PMID: 31569531 PMCID: PMC6835634 DOI: 10.3390/md17100561] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 11/17/2022] Open
Abstract
Cyanobacteria of the genus Nostoc are widespread in all kinds of habitats. They occur in a free-living state or in association with other organisms. Members of this genus belong to prolific producers of bioactive metabolites, some of which have been recognized as potential therapeutic agents. Of these, peptides and peptide-like structures show the most promising properties and are of a particular interest for both research laboratories and pharmaceutical companies. Nostoc is a sole source of some lead compounds such as cytotoxic cryptophycins, antiviral cyanovirin-N, or the antitoxic nostocyclopeptides. Nostoc also produces the same bioactive peptides as other cyanobacterial genera, but they frequently have some unique modifications in the structure. This includes hepatotoxic microcystins and potent proteases inhibitors such as cyanopeptolins, anabaenopeptins, and microginins. In this review, we described the most studied peptides produced by Nostoc, focusing especially on the structure, the activity, and a potential application of the compounds.
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Dehm D, Krumbholz J, Baunach M, Wiebach V, Hinrichs K, Guljamow A, Tabuchi T, Jenke-Kodama H, Süssmuth RD, Dittmann E. Unlocking the Spatial Control of Secondary Metabolism Uncovers Hidden Natural Product Diversity in Nostoc punctiforme. ACS Chem Biol 2019; 14:1271-1279. [PMID: 31091070 DOI: 10.1021/acschembio.9b00240] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Filamentous cyanobacteria belong to the most prolific producers of structurally unique and biologically active natural products, yet the majority of biosynthetic gene clusters predicted for these multicellular collectives are currently orphan. Here, we present a systems analysis of secondary metabolite gene expression in the model strain Nostoc punctiforme PCC73102 using RNA-seq and fluorescence reporter analysis. Our data demonstrate that the majority of the cryptic gene clusters are not silent but are expressed with regular or sporadic pattern. Cultivation of N. punctiforme using high-density fermentation overrules the spatial control and leads to a pronounced upregulation of more than 50% of biosynthetic gene clusters. Our data suggest that a combination of autocrine factors, a high CO2 level, and high light account for the upregulation of individual pathways. Our overarching study not only sheds light on the strategies of filamentous cyanobacteria to share the enormous metabolic burden connected with the production of specialized molecules but provides an avenue for the genome-based discovery of natural products in multicellular cyanobacteria as exemplified by the discovery of highly unusual variants of the tricyclic peptide microviridin.
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Affiliation(s)
- Daniel Dehm
- University of Potsdam , Institute for Biochemistry and Biology , Karl-Liebknecht-Str. 24/25 , 14476 Potsdam-Golm , Germany
| | - Julia Krumbholz
- University of Potsdam , Institute for Biochemistry and Biology , Karl-Liebknecht-Str. 24/25 , 14476 Potsdam-Golm , Germany
| | - Martin Baunach
- University of Potsdam , Institute for Biochemistry and Biology , Karl-Liebknecht-Str. 24/25 , 14476 Potsdam-Golm , Germany
| | - Vincent Wiebach
- Fakultät II - Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 124 , 10623 Berlin , Germany
| | - Katrin Hinrichs
- University of Potsdam , Institute for Biochemistry and Biology , Karl-Liebknecht-Str. 24/25 , 14476 Potsdam-Golm , Germany
| | - Arthur Guljamow
- University of Potsdam , Institute for Biochemistry and Biology , Karl-Liebknecht-Str. 24/25 , 14476 Potsdam-Golm , Germany
| | - Takeshi Tabuchi
- Microbiology and Biochemistry of Secondary Metabolites Unit . Okinawa Institute of Science and Technology , Tancha 1919-1 , Onna-son , 904-0495 Okinawa , Japan
| | - Holger Jenke-Kodama
- Microbiology and Biochemistry of Secondary Metabolites Unit . Okinawa Institute of Science and Technology , Tancha 1919-1 , Onna-son , 904-0495 Okinawa , Japan
| | - Roderich D Süssmuth
- Fakultät II - Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 124 , 10623 Berlin , Germany
| | - Elke Dittmann
- University of Potsdam , Institute for Biochemistry and Biology , Karl-Liebknecht-Str. 24/25 , 14476 Potsdam-Golm , Germany
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Huang IS, Zimba PV. Cyanobacterial bioactive metabolites-A review of their chemistry and biology. HARMFUL ALGAE 2019; 86:139-209. [PMID: 31358273 DOI: 10.1016/j.hal.2019.05.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/14/2018] [Accepted: 11/16/2018] [Indexed: 06/10/2023]
Abstract
Cyanobacterial blooms occur when algal densities exceed baseline population concentrations. Cyanobacteria can produce a large number of secondary metabolites. Odorous metabolites affect the smell and flavor of aquatic animals, whereas bioactive metabolites cause a range of lethal and sub-lethal effects in plants, invertebrates, and vertebrates, including humans. Herein, the bioactivity, chemistry, origin, and biosynthesis of these cyanobacterial secondary metabolites were reviewed. With recent revision of cyanobacterial taxonomy by Anagnostidis and Komárek as part of the Süβwasserflora von Mitteleuropa volumes 19(1-3), names of many cyanobacteria that produce bioactive compounds have changed, thereby confusing readers. The original and new nomenclature are included in this review to clarify the origins of cyanobacterial bioactive compounds. Due to structural similarity, the 157 known bioactive classes produced by cyanobacteria have been condensed to 55 classes. This review will provide a basis for more formal procedures to adopt a logical naming system. This review is needed for efficient management of water resources to understand, identify, and manage cyanobacterial harmful algal bloom impacts.
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Affiliation(s)
- I-Shuo Huang
- Center for Coastal Studies, Texas A&M University-Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA.
| | - Paul V Zimba
- Center for Coastal Studies, Texas A&M University-Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
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Miller TR, Bartlett SL, Weirich CA, Hernandez J. Automated Subdaily Sampling of Cyanobacterial Toxins on a Buoy Reveals New Temporal Patterns in Toxin Dynamics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:5661-5670. [PMID: 31038305 DOI: 10.1021/acs.est.9b00257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Temporal variability of toxins produced by cyanobacteria in lakes is relatively unknown at time scales relevant to public health (i.e., hourly). In this study, a water quality monitoring buoy was outfitted with an automated water sampler taking preserved samples every 6 h for 68.75 days over a drinking water intake. A total of 251 samples were analyzed by tandem mass spectrometry for 21 cyanotoxin congeners in 5 classes producing 5020 data points. Microcystins (MCs) were the most abundant toxins measured (mean ± sd = 3.9 ± 3.3 μg/L) followed by cyanopeptolins (CPs) (1.1 ± 1.5 μg/L), anabaenopeptins (APs) (1.0 ± 0.6 μg/L), anatoxin-a (AT-A) (0.03 ± 0.06 μg/L), and microginin-690 (MG-690) (0.002 ± 0.01 μg/L). Advanced time series analyses uncovered patterns in cyanotoxin production. The velocity of cyanotoxin concentration varied from -0.7 to 0.9 μg/L/h with a maximum positive velocity just prior to peak toxin concentration during nonbloom periods. A backward-looking moving window of variance analysis detected major increases in cyanotoxin concentration and predicted the two greatest increases in MC. A wavelet analysis identified a significant ( p < 0.01) 2.8-4.2 day periodicity in toxin concentration over a ∼25 day period during peak toxin production, which is partially explained by easterly wind velocity ( R = -0.2, p < 0.05). Diversity in congener profiles was explored with principle component analysis showing that cyanotoxin dynamics followed a seasonal trajectory where toxin profiles were significantly clustered (ANOSIM R = 0.7, p < 0.05) on a daily basis. Variability in toxin profiles was strongly correlated with time ( R = -0.8, p < 0.001) as well as the C:N ratio of the toxin pool ( R = 0.17, p < 0.05). The methods employed here should be useful for uncovering patterns in cyanotoxin dynamics in other systems.
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Affiliation(s)
- Todd R Miller
- Joseph J. Zilber School of Public Health , University of Wisconsin-Milwaukee , Milwaukee , Wisconsin 53211 , United States
| | - Sarah L Bartlett
- Joseph J. Zilber School of Public Health , University of Wisconsin-Milwaukee , Milwaukee , Wisconsin 53211 , United States
- School of Freshwater Sciences , University of Wisconsin-Milwaukee , Milwaukee , Wisconsin 53204 , United States
| | - Chelsea A Weirich
- Joseph J. Zilber School of Public Health , University of Wisconsin-Milwaukee , Milwaukee , Wisconsin 53211 , United States
| | - John Hernandez
- Joseph J. Zilber School of Public Health , University of Wisconsin-Milwaukee , Milwaukee , Wisconsin 53211 , United States
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40
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Kumar P, Hegde K, Brar SK, Cledon M, Kermanshahi-Pour A. Potential of biological approaches for cyanotoxin removal from drinking water: A review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 172:488-503. [PMID: 30738231 DOI: 10.1016/j.ecoenv.2019.01.066] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 01/20/2019] [Accepted: 01/22/2019] [Indexed: 05/20/2023]
Abstract
Biological treatment of cyanotoxins has gained much importance in recent decades and holds a promise to work in coordination with various physicochemical treatments. In drinking water treatment plants (DWTPs), effective removal of cyanotoxins with reduced toxicity is a primary concern. Commonly used treatments, such as ozonation, chlorination or activated carbon, undergo significant changes in their operating conditions (mainly dosage) to counter the variation in different environmental parameters, such as pH, temperature, and high cyanotoxin concentration. Presence of metal ions, natural organic matter (NOM), and other chemicals demand higher dosage and hence affect the activation energy to efficiently break down the cyanotoxin molecule. Due to these higher dose requirements, the treatment leads to the formation of toxic metabolites at a concentration high enough to break the guideline values. Biological methods of cyanotoxin removal proceed via enzymatic pathway where the protein-encoding genes are often responsible for the compound breakdown into non-toxic metabolites. However, in contrast to the chemical treatment, the biological processes advance at a much slower kinetic rate, predominantly due to a longer onset period (high lag phase). In fact, more than 90% of the studies reported on the biological degradation of the cyanotoxins attribute the biodegradation to the bacterial suspension. This suspended growth limits the mass transfer kinetics due to the presence of metal ions, NOMs and, other oxidizable matter, which further prolongs the lag phase and makes biological process toxic-free, albeit less efficient. In this context, this review attempts to bring out the importance of the attached growth mechanism, in particular, the biofilm-based treatment approaches which can enhance the biodegradation rate.
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Affiliation(s)
- Pratik Kumar
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, Canada G1K 9A9
| | | | - Satinder Kaur Brar
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, Canada G1K 9A9; Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, Ontario, Canada M3J 1P3.
| | - Maximiliano Cledon
- CIMAS (CONICET, UnComa, Rio Negro), Güemes 1030, San Antonio Oeste, Rio Negro, Argentina
| | - Azadeh Kermanshahi-Pour
- Biorefining and Remediation Laboratory, Department of Process Engineering and Applied Science, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia, Canada B3J 1Z1
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41
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Sinha S, Nge CE, Leong CY, Ng V, Crasta S, Alfatah M, Goh F, Low KN, Zhang H, Arumugam P, Lezhava A, Chen SL, Kanagasundaram Y, Ng SB, Eisenhaber F, Eisenhaber B. Genomics-driven discovery of a biosynthetic gene cluster required for the synthesis of BII-Rafflesfungin from the fungus Phoma sp. F3723. BMC Genomics 2019; 20:374. [PMID: 31088369 PMCID: PMC6518819 DOI: 10.1186/s12864-019-5762-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 05/02/2019] [Indexed: 12/20/2022] Open
Abstract
Background Phomafungin is a recently reported broad spectrum antifungal compound but its biosynthetic pathway is unknown. We combed publicly available Phoma genomes but failed to find any putative biosynthetic gene cluster that could account for its biosynthesis. Results Therefore, we sequenced the genome of one of our Phoma strains (F3723) previously identified as having antifungal activity in a high-throughput screen. We found a biosynthetic gene cluster that was predicted to synthesize a cyclic lipodepsipeptide that differs in the amino acid composition compared to Phomafungin. Antifungal activity guided isolation yielded a new compound, BII-Rafflesfungin, the structure of which was determined. Conclusions We describe the NRPS-t1PKS cluster ‘BIIRfg’ compatible with the synthesis of the cyclic lipodepsipeptide BII-Rafflesfungin [HMHDA-L-Ala-L-Glu-L-Asn-L-Ser-L-Ser-D-Ser-D-allo-Thr-Gly]. We report new Stachelhaus codes for Ala, Glu, Asn, Ser, Thr, and Gly. We propose a mechanism for BII-Rafflesfungin biosynthesis, which involves the formation of the lipid part by BIIRfg_PKS followed by activation and transfer of the lipid chain by a predicted AMP-ligase on to the first PCP domain of the BIIRfg_NRPS gene. Electronic supplementary material The online version of this article (10.1186/s12864-019-5762-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Swati Sinha
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
| | - Choy-Eng Nge
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Chung Yan Leong
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Veronica Ng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Sharon Crasta
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Mohammad Alfatah
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Falicia Goh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Kia-Ngee Low
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Huibin Zhang
- Genome Institue of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Republic of Singapore
| | - Prakash Arumugam
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Alexander Lezhava
- Genome Institue of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Republic of Singapore
| | - Swaine L Chen
- Genome Institue of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Republic of Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore, 119228, Republic of Singapore
| | - Yoganathan Kanagasundaram
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Siew Bee Ng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.,School of Computer Science and Engineering (SCSE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Republic of Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
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Shishido TK, Jokela J, Humisto A, Suurnäkki S, Wahlsten M, Alvarenga DO, Sivonen K, Fewer DP. The Biosynthesis of Rare Homo-Amino Acid Containing Variants of Microcystin by a Benthic Cyanobacterium. Mar Drugs 2019; 17:md17050271. [PMID: 31067786 PMCID: PMC6562525 DOI: 10.3390/md17050271] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/02/2019] [Accepted: 05/05/2019] [Indexed: 02/05/2023] Open
Abstract
Microcystins are a family of chemically diverse hepatotoxins produced by distantly related cyanobacteria and are potent inhibitors of eukaryotic protein phosphatases 1 and 2A. Here we provide evidence for the biosynthesis of rare variants of microcystin that contain a selection of homo-amino acids by the benthic cyanobacterium Phormidium sp. LP904c. This strain produces at least 16 microcystin chemical variants many of which contain homophenylalanine or homotyrosine. We retrieved the complete 54.2 kb microcystin (mcy) gene cluster from a draft genome assembly. Analysis of the substrate specificity of McyB1 and McyC adenylation domain binding pockets revealed divergent substrate specificity sequences, which could explain the activation of homo-amino acids which were present in 31% of the microcystins detected and included variants such as MC-LHty, MC-HphHty, MC-LHph and MC-HphHph. The mcy gene cluster did not encode enzymes for the synthesis of homo-amino acids but may instead activate homo-amino acids produced during the synthesis of anabaenopeptins. We observed the loss of microcystin during cultivation of a closely related strain, Phormidium sp. DVL1003c. This study increases the knowledge of benthic cyanobacterial strains that produce microcystin variants and broadens the structural diversity of known microcystins.
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Affiliation(s)
- Tânia Keiko Shishido
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-0014 Helsinki, Finland.
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Viikinkaari 5D, FI-0014 Helsinki, Finland.
| | - Jouni Jokela
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-0014 Helsinki, Finland.
| | - Anu Humisto
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-0014 Helsinki, Finland.
| | - Suvi Suurnäkki
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-0014 Helsinki, Finland.
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014 Jyväskylä, Finland.
| | - Matti Wahlsten
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-0014 Helsinki, Finland.
| | - Danillo O Alvarenga
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-0014 Helsinki, Finland.
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-0014 Helsinki, Finland.
| | - David P Fewer
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-0014 Helsinki, Finland.
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Cook TB, Pfleger BF. Leveraging synthetic biology for producing bioactive polyketides and non-ribosomal peptides in bacterial heterologous hosts. MEDCHEMCOMM 2019; 10:668-681. [PMID: 31191858 PMCID: PMC6540960 DOI: 10.1039/c9md00055k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/06/2019] [Indexed: 12/14/2022]
Abstract
Bacteria have historically been a rich source of natural products (e.g. polyketides and non-ribosomal peptides) that possess medically-relevant activities. Despite extensive discovery programs in both industry and academia, a plethora of biosynthetic pathways remain uncharacterized and the corresponding molecular products untested for potential bioactivities. This knowledge gap comes in part from the fact that many putative natural product producers have not been cultured in conventional laboratory settings in which the corresponding products are produced at detectable levels. Next-generation sequencing technologies are further increasing the knowledge gap by obtaining metagenomic sequence information from complex communities where production of the desired compound cannot be isolated in the laboratory. For these reasons, many groups are turning to synthetic biology to produce putative natural products in heterologous hosts. This strategy depends on the ability to heterologously express putative biosynthetic gene clusters and produce relevant quantities of the corresponding products. Actinobacteria remain the most abundant source of natural products and the most promising heterologous hosts for natural product discovery and production. However, researchers are discovering more natural products from other groups of bacteria, such as myxobacteria and cyanobacteria. Therefore, phylogenetically similar heterologous hosts have become promising candidates for synthesizing these novel molecules. The downside of working with these microbes is the lack of well-characterized genetic tools for optimizing expression of gene clusters and product titers. This review examines heterologous expression of natural product gene clusters in terms of the motivations for this research, the traits desired in an ideal host, tools available to the field, and a survey of recent progress.
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Affiliation(s)
- Taylor B Cook
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Dr. Room 3629 , Madison , WI 53706 , USA .
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Dr. Room 3629 , Madison , WI 53706 , USA .
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Pawlik-Skowrońska B, Toporowska M, Mazur-Marzec H. Effects of secondary metabolites produced by different cyanobacterial populations on the freshwater zooplankters Brachionus calyciflorus and Daphnia pulex. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:11793-11804. [PMID: 30815809 PMCID: PMC6476996 DOI: 10.1007/s11356-019-04543-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/13/2019] [Indexed: 05/16/2023]
Abstract
Cyanobacterial blooms in eutrophic water bodies are a worldwide problem. Combined effects of mixtures of secondary metabolites produced by different cyanobacterial species on aquatic fauna are still not well recognised. We compared the survivorship of Brachionus calyciflorus Pallas (Rotifera) and Daphnia pulex Leyding (Cladocera) exposed to pure microcystin LR (MC-LR), anatoxin-a (ANTX) and to five extracts obtained from bloom-forming cyanobacteria Microcystis, Planktothrix and Dolichospermum. The obtained results revealed different response of the organisms to high concentrations of pure MC-LR, ANTX and complex cyanobacterial extracts. The extracts' toxicity to invertebrates was higher than that exerted by pure cyanotoxins and was dependent on the composition of cyanobacterial metabolites: Microcystis spp. extract containing anabaenopeptins A and B, aeruginosamide, four variants of cyanopeptolins and five MCs was not toxic to either of the organisms, whereas Planktothrix agardhii extract (I), containing anabaenopeptins A, B, F, 915, oscillamide Y, five different aeruginosins and four variants of MC was more toxic to daphnids than to rotifers. The extracts of another P. agarhdii (II) biomass and two different biomass samples of Dolichospermum spp. also affected survivorship of the rotifer and cladoceran, however, to various extent. It strongly suggests that non-ribosomal oligopeptides, other than MCs, had essential contribution to the observed toxicity to invertebrates and their effects on particular species or populations can vary depending on the secondary metabolite profiles of cyanobacteria.
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Affiliation(s)
- Barbara Pawlik-Skowrońska
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37, 20-262 Lublin, Poland
| | - Magdalena Toporowska
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37, 20-262 Lublin, Poland
| | - Hanna Mazur-Marzec
- Division of Marine Biotechnology, University of Gdańsk, al. Piłsudskiego 46, 81-378 Gdynia, Poland
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Huang IS, Zimba PV. Cyanobacterial bioactive metabolites-A review of their chemistry and biology. HARMFUL ALGAE 2019; 83:42-94. [PMID: 31097255 DOI: 10.1016/j.hal.2018.11.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/14/2018] [Accepted: 11/16/2018] [Indexed: 06/09/2023]
Abstract
Cyanobacterial blooms occur when algal densities exceed baseline population concentrations. Cyanobacteria can produce a large number of secondary metabolites. Odorous metabolites affect the smell and flavor of aquatic animals, whereas bioactive metabolites cause a range of lethal and sub-lethal effects in plants, invertebrates, and vertebrates, including humans. Herein, the bioactivity, chemistry, origin, and biosynthesis of these cyanobacterial secondary metabolites were reviewed. With recent revision of cyanobacterial taxonomy by Anagnostidis and Komárek as part of the Süβwasserflora von Mitteleuropa volumes 19(1-3), names of many cyanobacteria that produce bioactive compounds have changed, thereby confusing readers. The original and new nomenclature are included in this review to clarify the origins of cyanobacterial bioactive compounds. Due to structural similarity, the 157 known bioactive classes produced by cyanobacteria have been condensed to 55 classes. This review will provide a basis for more formal procedures to adopt a logical naming system. This review is needed for efficient management of water resources to understand, identify, and manage cyanobacterial harmful algal bloom impacts.
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Affiliation(s)
- I-Shuo Huang
- Center for Coastal Studies, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA.
| | - Paul V Zimba
- Center for Coastal Studies, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
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Alternative Biosynthetic Starter Units Enhance the Structural Diversity of Cyanobacterial Lipopeptides. Appl Environ Microbiol 2019; 85:AEM.02675-18. [PMID: 30504214 DOI: 10.1128/aem.02675-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/28/2018] [Indexed: 12/24/2022] Open
Abstract
Puwainaphycins (PUWs) and minutissamides (MINs) are structurally analogous cyclic lipopeptides possessing cytotoxic activity. Both types of compound exhibit high structural variability, particularly in the fatty acid (FA) moiety. Although a biosynthetic gene cluster responsible for synthesis of several PUW variants has been proposed in a cyanobacterial strain, the genetic background for MINs remains unexplored. Herein, we report PUW/MIN biosynthetic gene clusters and structural variants from six cyanobacterial strains. Comparison of biosynthetic gene clusters indicates a common origin of the PUW/MIN hybrid nonribosomal peptide synthetase and polyketide synthase. Surprisingly, the biosynthetic gene clusters encode two alternative biosynthetic starter modules, and analysis of structural variants suggests that initiation by each of the starter modules results in lipopeptides of differing lengths and FA substitutions. Among additional modifications of the FA chain, chlorination of minutissamide D was explained by the presence of a putative halogenase gene in the PUW/MIN gene cluster of Anabaena minutissima strain UTEX B 1613. We detected PUW variants bearing an acetyl substitution in Symplocastrum muelleri strain NIVA-CYA 644, consistent with an O-acetyltransferase gene in its biosynthetic gene cluster. The major lipopeptide variants did not exhibit any significant antibacterial activity, and only the PUW F variant was moderately active against yeast, consistent with previously published data suggesting that PUWs/MINs interact preferentially with eukaryotic plasma membranes.IMPORTANCE Herein, we deciphered the most important biosynthetic traits of a prominent group of bioactive lipopeptides. We reveal evidence for initiation of biosynthesis by two alternative starter units hardwired directly in the same gene cluster, eventually resulting in the production of a remarkable range of lipopeptide variants. We identified several unusual tailoring genes potentially involved in modifying the fatty acid chain. Careful characterization of these biosynthetic gene clusters and their diverse products could provide important insight into lipopeptide biosynthesis in prokaryotes. Some of the variants identified exhibit cytotoxic and antifungal properties, and some are associated with a toxigenic biofilm-forming strain. The findings may prove valuable to researchers in the fields of natural product discovery and toxicology.
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Pancrace C, Ishida K, Briand E, Pichi DG, Weiz AR, Guljamow A, Scalvenzi T, Sassoon N, Hertweck C, Dittmann E, Gugger M. Unique Biosynthetic Pathway in Bloom-Forming Cyanobacterial Genus Microcystis Jointly Assembles Cytotoxic Aeruginoguanidines and Microguanidines. ACS Chem Biol 2019; 14:67-75. [PMID: 30556994 DOI: 10.1021/acschembio.8b00918] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The cyanobacterial genus Microcystis is known to produce an elaborate array of structurally unique and biologically active natural products, including hazardous cyanotoxins. Cytotoxic aeruginoguanidines represent a yet unexplored family of peptides featuring a trisubstituted benzene unit and farnesylated arginine derivatives. In this study, we aimed at assigning these compounds to a biosynthetic gene cluster by utilizing biosynthetic attributes deduced from public genomes of Microcystis and the sporadic distribution of the metabolite in axenic strains of the Pasteur Culture Collection of Cyanobacteria. By integrating genome mining with untargeted metabolomics using liquid chromatography with mass spectrometry, we linked aeruginoguanidine (AGD) to a nonribosomal peptide synthetase gene cluster and coassigned a significantly smaller product to this pathway, microguanidine (MGD), previously only reported from two Microcystis blooms. Further, a new intermediate class of compounds named microguanidine amides was uncovered, thereby further enlarging this compound family. The comparison of structurally divergent AGDs and MGDs reveals an outstanding versatility of this biosynthetic pathway and provides insights into the assembly of the two compound subfamilies. Strikingly, aeruginoguanidines and microguanidines were found to be as widespread as the hepatotoxic microcystins, but the occurrence of both toxin families appeared to be mutually exclusive.
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Affiliation(s)
- Claire Pancrace
- Collection des Cyanobactéries, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
- UMR UPMC 113, CNRS 7618, IRD 242, INRA 1392, PARIS 7 113, UPEC, IEES Paris, 4 Place Jussieu, 75005 Paris, France
| | - Keishi Ishida
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Enora Briand
- Laboratoire Phycotoxines, Ifremer, rue de l’Ile d’Yeu, 44311 Nantes, France
| | - Douglas Gatte Pichi
- Department of Microbiology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Golm, Germany
| | - Annika R. Weiz
- Department of Microbiology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Golm, Germany
| | - Arthur Guljamow
- Department of Microbiology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Golm, Germany
| | - Thibault Scalvenzi
- Collection des Cyanobactéries, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Nathalie Sassoon
- Collection des Cyanobactéries, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Elke Dittmann
- Department of Microbiology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Golm, Germany
| | - Muriel Gugger
- Collection des Cyanobactéries, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
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Driscoll CB, Meyer KA, Šulčius S, Brown NM, Dick GJ, Cao H, Gasiūnas G, Timinskas A, Yin Y, Landry ZC, Otten TG, Davis TW, Watson SB, Dreher TW. A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales. HARMFUL ALGAE 2018; 77:93-107. [PMID: 30005805 DOI: 10.1016/j.hal.2018.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/18/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
In order to better understand the relationships among current Nostocales cyanobacterial blooms, eight genomes were sequenced from cultured isolates or from environmental metagenomes of recent planktonic Nostocales blooms. Phylogenomic analysis of publicly available sequences placed the new genomes among a group of 15 genomes from four continents in a distinct ADA clade (Anabaena/Dolichospermum/Aphanizomenon) within the Nostocales. This clade contains four species-level groups, two of which include members with both Anabaena-like and Aphanizomenon flos-aquae-like morphology. The genomes contain many repetitive genetic elements and a sizable pangenome, in which ABC-type transporters are highly represented. Alongside common core genes for photosynthesis, the differentiation of N2-fixing heterocysts, and the uptake and incorporation of the major nutrients P, N and S, we identified several gene pathways in the pangenome that may contribute to niche partitioning. Genes for problematic secondary metabolites-cyanotoxins and taste-and-odor compounds-were sporadically present, as were other polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters. By contrast, genes predicted to encode the ribosomally generated bacteriocin peptides were found in all genomes.
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Affiliation(s)
- Connor B Driscoll
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Kevin A Meyer
- Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, MI 48109-1005, USA; Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI 48109-1005, USA
| | - Sigitas Šulčius
- Laboratory of Algology and Microbial Ecology, Akademijos Str. 2, LT-08412, Vilnius, Lithuania
| | - Nathan M Brown
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Gregory J Dick
- Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, MI 48109-1005, USA
| | - Huansheng Cao
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA
| | - Giedrius Gasiūnas
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania
| | - Albertas Timinskas
- Department of Bioinformatics, Institute of Biotechnology, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Yanbin Yin
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Zachary C Landry
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Timothy G Otten
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Timothy W Davis
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43402, USA
| | - Susan B Watson
- Environment and Climate Change Canada, Canada Centre for Inland Waters, Burlington, ON L7S 1A1, Canada
| | - Theo W Dreher
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.
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49
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Tobias NJ, Linck A, Bode HB. Natural Product Diversification Mediated by Alternative Transcriptional Starting. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nicholas J. Tobias
- Fachbereich Biowissenschaften; Merck Stiftungsprofessur für Molekulare Biotechnologie; Goethe-Universität Frankfurt; Frankfurt am Main Germany
| | - Annabell Linck
- Fachbereich Biowissenschaften; Merck Stiftungsprofessur für Molekulare Biotechnologie; Goethe-Universität Frankfurt; Frankfurt am Main Germany
| | - Helge B. Bode
- Fachbereich Biowissenschaften; Merck Stiftungsprofessur für Molekulare Biotechnologie; Goethe-Universität Frankfurt; Frankfurt am Main Germany
- Buchmann Institute for Molecular Life Sciences; Goethe-Universität Frankfurt; Frankfurt am Main Germany
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50
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Greunke C, Duell ER, D’Agostino PM, Glöckle A, Lamm K, Gulder TAM. Direct Pathway Cloning (DiPaC) to unlock natural product biosynthetic potential. Metab Eng 2018; 47:334-345. [DOI: 10.1016/j.ymben.2018.03.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/04/2018] [Accepted: 03/11/2018] [Indexed: 12/12/2022]
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